Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.29, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 361.0 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 731 0.94 - 1.21: 965 1.21 - 1.47: 787 1.47 - 1.74: 658 1.74 - 2.01: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.340 1.189 0.151 6.60e-03 2.30e+04 5.24e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.519 1.303 0.216 1.04e-02 9.25e+03 4.30e+02 bond pdb=" C ASP A 149 " pdb=" O ASP A 149 " ideal model delta sigma weight residual 1.235 1.020 0.215 1.14e-02 7.69e+03 3.55e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.234 1.026 0.209 1.11e-02 8.12e+03 3.53e+02 bond pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 1.330 1.087 0.243 1.30e-02 5.92e+03 3.49e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3018 4.49 - 8.97: 1903 8.97 - 13.46: 684 13.46 - 17.95: 152 17.95 - 22.44: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 113.83 7.24 3.60e-01 7.72e+00 4.04e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 106.42 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" CA VAL A 23 " pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 121.27 135.78 -14.51 1.04e+00 9.25e-01 1.95e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 126.44 -13.84 1.00e+00 1.00e+00 1.91e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 108.37 14.83 1.08e+00 8.57e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 925 16.17 - 32.33: 121 32.33 - 48.50: 42 48.50 - 64.67: 19 64.67 - 80.83: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.207: 102 0.207 - 0.412: 72 0.412 - 0.616: 45 0.616 - 0.821: 22 0.821 - 1.026: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA VAL A 181 " pdb=" N VAL A 181 " pdb=" C VAL A 181 " pdb=" CB VAL A 181 " both_signs ideal model delta sigma weight residual False 2.44 3.26 -0.82 2.00e-01 2.50e+01 1.68e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.119 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.132 9.50e-02 1.11e+02 8.48e-02 1.20e+02 pdb=" NE ARG A 5 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.106 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.105 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.069 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.106 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.050 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.107 2.00e-02 2.50e+03 5.45e-02 8.92e+01 pdb=" CG ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.000 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.013 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 635 2.26 - 2.84: 7701 2.84 - 3.43: 10630 3.43 - 4.01: 15493 4.01 - 4.60: 22152 Nonbonded interactions: 56611 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.673 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 2.450 nonbonded pdb=" HG3BGLU A 90 " pdb=" O HOH A 373 " model vdw 1.848 2.620 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.851 2.450 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.855 2.450 ... (remaining 56606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_4912670_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1911 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793428 | | target function (ml) not normalized (work): 232709.303819 | | target function (ml) not normalized (free): 11808.384591 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3031 0.2038 7.1204 4.9365| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1728 4.3445 4.3334| | 3: 2.84 - 2.48 1.00 2833 165 0.2354 0.1635 4.1198 4.1455| | 4: 2.47 - 2.25 1.00 2825 136 0.2353 0.1453 3.8277 3.8263| | 5: 2.25 - 2.09 1.00 2756 127 0.2492 0.1498 3.7913 3.8047| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1712 3.4539 3.5946| | 7: 1.97 - 1.87 1.00 2787 165 0.2584 0.1852 3.1437 3.1889| | 8: 1.87 - 1.79 1.00 2789 144 0.2429 0.1757 3.0534 3.0821| | 9: 1.79 - 1.72 1.00 2745 138 0.2392 0.1739 2.9012 2.8788| | 10: 1.72 - 1.66 1.00 2789 158 0.2396 0.1892 2.8017 2.8562| | 11: 1.66 - 1.61 1.00 2740 147 0.2529 0.1820 2.744 2.7311| | 12: 1.61 - 1.56 1.00 2787 146 0.2492 0.1945 2.6216 2.6455| | 13: 1.56 - 1.52 1.00 2745 130 0.2599 0.1988 2.577 2.647| | 14: 1.52 - 1.48 1.00 2803 134 0.2544 0.1822 2.5096 2.4728| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.1820 2.446 2.3654| | 16: 1.45 - 1.42 1.00 2756 161 0.2632 0.2286 2.3684 2.4752| | 17: 1.42 - 1.39 1.00 2785 139 0.2659 0.2184 2.3201 2.3949| | 18: 1.39 - 1.36 1.00 2741 179 0.2763 0.2341 2.2832 2.3951| | 19: 1.36 - 1.34 1.00 2807 134 0.2691 0.2592 2.2577 2.3424| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2328 2.2146 2.2498| | 21: 1.32 - 1.30 1.00 2785 112 0.2724 0.2218 2.1682 2.1623| | 22: 1.29 - 1.27 1.00 2704 152 0.2764 0.2612 2.1369 2.2332| | 23: 1.27 - 1.26 1.00 2802 156 0.2756 0.2491 2.1052 2.1711| | 24: 1.26 - 1.24 1.00 2744 132 0.2805 0.2475 2.0843 2.1278| | 25: 1.24 - 1.22 1.00 2734 148 0.2787 0.2472 2.0517 2.0806| | 26: 1.22 - 1.21 1.00 2727 135 0.2873 0.2268 2.0087 2.0875| | 27: 1.21 - 1.19 1.00 2814 148 0.2996 0.2995 2.0167 2.1091| | 28: 1.19 - 1.18 1.00 2671 147 0.2982 0.2575 1.9838 1.9492| | 29: 1.18 - 1.16 1.00 2800 134 0.2954 0.2666 1.9603 2.0135| | 30: 1.16 - 1.15 1.00 2740 148 0.3108 0.2952 1.9291 1.9807| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.49 0.76 0.23 1441.40| | 2: 3.57 - 2.84 2876 122 0.81 25.85 1.27 0.23 1441.40| | 3: 2.84 - 2.48 2833 165 0.74 31.70 1.24 0.23 1195.94| | 4: 2.47 - 2.25 2825 136 0.82 25.27 1.26 0.25 558.94| | 5: 2.25 - 2.09 2756 127 0.78 28.94 1.29 0.25 558.94| | 6: 2.09 - 1.97 2846 113 0.84 22.50 1.29 0.25 306.75| | 7: 1.97 - 1.87 2787 165 0.90 16.81 1.29 0.25 91.67| | 8: 1.87 - 1.79 2789 144 0.86 21.23 1.24 0.25 91.67| | 9: 1.79 - 1.72 2745 138 0.88 18.09 1.22 0.25 53.16| | 10: 1.72 - 1.66 2789 158 0.87 19.71 1.21 0.25 45.44| | 11: 1.66 - 1.61 2740 147 0.86 20.82 1.24 0.25 43.92| | 12: 1.61 - 1.56 2787 146 0.89 18.04 1.23 0.25 28.45| | 13: 1.56 - 1.52 2745 130 0.87 20.09 1.24 0.25 28.45| | 14: 1.52 - 1.48 2803 134 0.87 20.37 1.22 0.25 25.67| | 15: 1.48 - 1.45 2738 128 0.87 19.99 1.23 0.25 20.57| | 16: 1.45 - 1.42 2756 161 0.85 21.73 1.24 0.25 20.57| | 17: 1.42 - 1.39 2785 139 0.86 21.45 1.23 0.25 18.00| | 18: 1.39 - 1.36 2741 179 0.86 21.95 1.24 0.24 16.50| | 19: 1.36 - 1.34 2807 134 0.85 22.81 1.22 0.24 16.50| | 20: 1.34 - 1.32 2696 147 0.86 21.91 1.20 0.24 13.82| | 21: 1.32 - 1.30 2785 112 0.85 22.78 1.20 0.24 13.63| | 22: 1.29 - 1.27 2704 152 0.84 23.69 1.22 0.24 13.32| | 23: 1.27 - 1.26 2802 156 0.85 22.92 1.21 0.24 11.71| | 24: 1.26 - 1.24 2744 132 0.84 23.78 1.20 0.24 11.71| | 25: 1.24 - 1.22 2734 148 0.84 23.94 1.19 0.24 11.02| | 26: 1.22 - 1.21 2727 135 0.83 24.62 1.20 0.23 10.26| | 27: 1.21 - 1.19 2814 148 0.83 25.29 1.20 0.23 10.26| | 28: 1.19 - 1.18 2671 147 0.83 25.16 1.18 0.23 9.29| | 29: 1.18 - 1.16 2800 134 0.83 25.27 1.16 0.23 8.92| | 30: 1.16 - 1.15 2740 148 0.81 27.05 1.17 0.23 8.92| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.92 max = 1441.40 mean = 209.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.74| |phase err.(test): min = 0.00 max = 89.47 mean = 22.63| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.243 1557 Z= 5.444 Angle : 5.386 18.870 2118 Z= 3.769 Chirality : 0.364 1.026 243 Planarity : 0.031 0.082 284 Dihedral : 14.033 80.833 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.47), residues: 224 helix: -2.91 (0.33), residues: 102 sheet: -0.96 (0.72), residues: 38 loop : -0.27 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.013 ARG A 145 TYR 0.073 0.030 TYR A 139 PHE 0.111 0.049 PHE A 119 HIS 0.079 0.048 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1911 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793428 | | target function (ml) not normalized (work): 232709.303819 | | target function (ml) not normalized (free): 11808.384591 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2612 0.1911 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2612 0.1911 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1991 0.1911 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2008 0.2014 0.1925 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1649 0.1644 0.1744 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1644 0.1744 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3830 386.266 357.617 0.682 1.003 0.411 11.894-9.307 99.02 97 4 0.1827 613.565 594.155 0.934 1.003 0.378 9.237-7.194 100.00 213 7 0.2184 501.821 490.231 0.960 1.003 0.339 7.162-5.571 100.00 427 22 0.2240 376.589 362.430 0.931 1.003 0.288 5.546-4.326 100.00 867 58 0.1275 516.963 511.494 0.965 1.003 0.234 4.315-3.360 100.00 1859 96 0.1132 491.636 488.487 1.009 1.003 0.209 3.356-2.611 100.00 3867 181 0.1447 322.979 319.149 0.997 1.002 0.109 2.608-2.026 99.99 8198 413 0.1358 214.106 212.192 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1650 104.558 103.908 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2085 46.365 45.007 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2588 29.213 26.919 0.977 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0443 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1744 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1645 r_free=0.1745 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.905167 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2028.521615 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1458 0.0248 0.008 1.0 1.0 0.5 0.0 0 13.953 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.58 2.48 3.013 19.052 2028.522 0.017 12.42 15.37 2.95 3.329 19.605 2028.522 0.016 Individual atomic B min max mean iso aniso Overall: 8.50 118.58 21.13 2.88 0 1785 Protein: 8.50 118.58 17.96 2.88 0 1519 Water: 11.07 114.49 39.47 N/A 0 258 Other: 23.38 37.45 29.98 N/A 0 8 Chain A: 8.50 118.58 21.13 N/A 0 1785 Histogram: Values Number of atoms 8.50 - 19.51 1203 19.51 - 30.52 231 30.52 - 41.53 160 41.53 - 52.53 105 52.53 - 63.54 53 63.54 - 74.55 17 74.55 - 85.56 9 85.56 - 96.56 2 96.56 - 107.57 2 107.57 - 118.58 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1537 r_work=0.1247 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 r_free = 0.1542 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1544 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015370 | | target function (ls_wunit_k1) not normalized (work): 1280.251774 | | target function (ls_wunit_k1) not normalized (free): 114.046520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1247 0.1544 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1699 0.1697 0.1763 n_refl.: 87593 remove outliers: r(all,work,free)=0.1699 0.1697 0.1763 n_refl.: 87593 overall B=0.15 to atoms: r(all,work,free)=0.1722 0.1722 0.1779 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1538 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1244 0.1538 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3561 295.581 279.067 0.625 1.003 0.372 11.894-9.307 99.02 97 4 0.1631 478.972 467.424 0.904 1.003 0.367 9.237-7.194 100.00 213 7 0.1822 391.740 386.279 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1709 293.979 288.729 0.923 1.003 0.253 5.546-4.326 100.00 867 58 0.0913 403.560 400.940 0.950 1.003 0.220 4.315-3.360 100.00 1859 96 0.0769 383.789 382.832 0.996 1.003 0.189 3.356-2.611 100.00 3867 181 0.1019 252.129 251.464 0.998 1.002 0.110 2.608-2.026 99.99 8198 413 0.0981 167.139 166.509 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1218 81.622 81.800 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1652 36.194 35.659 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2358 22.805 21.316 0.969 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0572 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1246 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1538 | n_water=258 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1256 r_free=0.1536 | n_water=251 | time (s): 26.440 (total time: 28.890) Filter (q & B) r_work=0.1259 r_free=0.1535 | n_water=248 | time (s): 3.710 (total time: 32.600) Compute maps r_work=0.1259 r_free=0.1535 | n_water=248 | time (s): 1.870 (total time: 34.470) Filter (map) r_work=0.1274 r_free=0.1539 | n_water=236 | time (s): 3.970 (total time: 38.440) Find peaks r_work=0.1274 r_free=0.1539 | n_water=236 | time (s): 0.770 (total time: 39.210) Add new water r_work=0.1430 r_free=0.1692 | n_water=452 | time (s): 3.900 (total time: 43.110) Refine new water occ: r_work=0.1335 r_free=0.1571 adp: r_work=0.1259 r_free=0.1517 occ: r_work=0.1270 r_free=0.1516 adp: r_work=0.1237 r_free=0.1499 occ: r_work=0.1240 r_free=0.1502 adp: r_work=0.1231 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1499 r_work=0.1231 r_free=0.1499 | n_water=452 | time (s): 104.420 (total time: 147.530) Filter (q & B) r_work=0.1236 r_free=0.1504 | n_water=426 | time (s): 4.080 (total time: 151.610) Filter (dist only) r_work=0.1236 r_free=0.1504 | n_water=426 | time (s): 40.310 (total time: 191.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.746733 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1472.210771 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1532 0.0300 0.007 0.9 1.9 0.5 0.0 0 12.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.32 3.00 3.811 23.265 1472.211 0.015 12.09 15.10 3.00 4.228 23.060 1472.211 0.015 Individual atomic B min max mean iso aniso Overall: 8.79 113.90 23.20 2.59 190 1763 Protein: 8.79 113.90 17.75 2.59 0 1519 Water: 10.93 73.96 42.53 N/A 190 236 Other: 21.67 34.64 27.30 N/A 0 8 Chain A: 8.79 113.90 20.48 N/A 0 1763 Chain S: 19.43 70.46 48.38 N/A 190 0 Histogram: Values Number of atoms 8.79 - 19.30 1206 19.30 - 29.81 249 29.81 - 40.32 178 40.32 - 50.83 145 50.83 - 61.34 111 61.34 - 71.85 51 71.85 - 82.37 7 82.37 - 92.88 3 92.88 - 103.39 1 103.39 - 113.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1510 r_work=0.1209 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1509 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1507 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014052 | | target function (ls_wunit_k1) not normalized (work): 1170.424831 | | target function (ls_wunit_k1) not normalized (free): 109.245240 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1209 0.1507 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1607 0.1601 0.1737 n_refl.: 87591 remove outliers: r(all,work,free)=0.1607 0.1601 0.1737 n_refl.: 87591 overall B=0.05 to atoms: r(all,work,free)=0.1615 0.1610 0.1743 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1206 0.1502 n_refl.: 87591 remove outliers: r(all,work,free)=0.1220 0.1205 0.1502 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3432 294.931 268.511 0.602 0.938 0.350 11.894-9.307 99.02 97 4 0.1646 478.972 475.952 0.970 0.939 0.334 9.237-7.194 100.00 213 7 0.1734 391.740 390.700 1.041 0.939 0.300 7.162-5.571 100.00 427 22 0.1497 293.979 290.340 1.000 0.940 0.219 5.546-4.326 100.00 867 58 0.0807 403.560 400.947 1.020 0.940 0.210 4.315-3.360 100.00 1859 96 0.0714 383.789 382.683 1.068 0.941 0.200 3.356-2.611 100.00 3867 181 0.0946 252.129 251.480 1.073 0.942 0.072 2.608-2.026 99.99 8198 413 0.0969 167.139 166.717 1.079 0.943 0.000 2.025-1.573 100.00 17313 902 0.1198 81.622 81.816 1.084 0.946 0.000 1.573-1.221 100.00 36679 1900 0.1630 36.194 35.685 1.063 0.951 0.000 1.221-1.150 99.97 13689 708 0.2349 22.805 21.358 1.017 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0812 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1502 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1502 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1502 | n_water=426 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1208 r_free=0.1499 | n_water=424 | time (s): 36.080 (total time: 38.010) Filter (q & B) r_work=0.1208 r_free=0.1499 | n_water=424 | time (s): 1.240 (total time: 39.250) Compute maps r_work=0.1208 r_free=0.1499 | n_water=424 | time (s): 1.810 (total time: 41.060) Filter (map) r_work=0.1251 r_free=0.1498 | n_water=284 | time (s): 2.810 (total time: 43.870) Find peaks r_work=0.1251 r_free=0.1498 | n_water=284 | time (s): 0.500 (total time: 44.370) Add new water r_work=0.1376 r_free=0.1608 | n_water=476 | time (s): 2.930 (total time: 47.300) Refine new water occ: r_work=0.1273 r_free=0.1522 adp: r_work=0.1274 r_free=0.1520 occ: r_work=0.1252 r_free=0.1507 adp: r_work=0.1249 r_free=0.1504 occ: r_work=0.1237 r_free=0.1496 adp: r_work=0.1230 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1490 r_work=0.1230 r_free=0.1490 | n_water=476 | time (s): 180.870 (total time: 228.170) Filter (q & B) r_work=0.1233 r_free=0.1498 | n_water=441 | time (s): 3.470 (total time: 231.640) Filter (dist only) r_work=0.1233 r_free=0.1498 | n_water=441 | time (s): 36.000 (total time: 267.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.054934 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 56.213635 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1460 0.0223 0.005 0.9 1.6 0.5 0.0 0 1.027 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.60 2.23 3.632 22.156 56.214 3.735 12.09 14.09 2.00 4.179 21.946 56.214 3.653 Individual atomic B min max mean iso aniso Overall: 9.21 108.95 21.61 2.37 210 1758 Protein: 9.21 108.95 17.29 2.37 0 1519 Water: 11.56 72.88 36.46 N/A 210 231 Other: 18.17 30.63 24.56 N/A 0 8 Chain A: 9.21 108.95 19.93 N/A 0 1758 Chain S: 15.88 65.48 35.66 N/A 210 0 Histogram: Values Number of atoms 9.21 - 19.18 1228 19.18 - 29.16 279 29.16 - 39.13 216 39.13 - 49.11 133 49.11 - 59.08 76 59.08 - 69.05 23 69.05 - 79.03 7 79.03 - 89.00 3 89.00 - 98.98 1 98.98 - 108.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1409 r_work=0.1210 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1410 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1409 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1409 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651623 | | target function (ml) not normalized (work): 304154.622375 | | target function (ml) not normalized (free): 16075.404896 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1207 0.1409 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1536 0.1535 0.1581 n_refl.: 87589 remove outliers: r(all,work,free)=0.1536 0.1535 0.1581 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1535 0.1534 0.1580 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1198 0.1385 n_refl.: 87589 remove outliers: r(all,work,free)=0.1205 0.1196 0.1385 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3825 299.773 262.888 0.481 1.001 0.330 11.894-9.307 99.02 97 4 0.2421 478.972 464.201 0.852 1.002 0.330 9.237-7.194 98.18 209 7 0.2334 386.375 385.929 0.953 1.002 0.180 7.162-5.571 100.00 427 22 0.2058 293.979 283.902 0.922 1.002 0.158 5.546-4.326 100.00 867 58 0.1102 403.560 398.705 0.959 1.002 0.151 4.315-3.360 100.00 1859 96 0.0927 383.789 381.202 1.005 1.002 0.147 3.356-2.611 100.00 3867 181 0.1151 252.129 250.287 1.011 1.002 0.062 2.608-2.026 99.99 8198 413 0.1042 167.139 166.161 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1015 81.622 81.764 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1288 36.194 35.775 1.029 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.805 21.428 0.986 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0186 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1385 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1385 | n_water=441 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1196 r_free=0.1385 | n_water=441 | time (s): 36.680 (total time: 38.520) Filter (q & B) r_work=0.1196 r_free=0.1387 | n_water=438 | time (s): 2.410 (total time: 40.930) Compute maps r_work=0.1196 r_free=0.1387 | n_water=438 | time (s): 1.440 (total time: 42.370) Filter (map) r_work=0.1222 r_free=0.1386 | n_water=312 | time (s): 3.470 (total time: 45.840) Find peaks r_work=0.1222 r_free=0.1386 | n_water=312 | time (s): 0.630 (total time: 46.470) Add new water r_work=0.1283 r_free=0.1459 | n_water=468 | time (s): 3.560 (total time: 50.030) Refine new water occ: r_work=0.1212 r_free=0.1381 adp: r_work=0.1213 r_free=0.1385 occ: r_work=0.1197 r_free=0.1361 adp: r_work=0.1196 r_free=0.1365 occ: r_work=0.1186 r_free=0.1346 adp: r_work=0.1183 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1349 r_work=0.1183 r_free=0.1349 | n_water=468 | time (s): 178.490 (total time: 228.520) Filter (q & B) r_work=0.1189 r_free=0.1351 | n_water=438 | time (s): 3.320 (total time: 231.840) Filter (dist only) r_work=0.1189 r_free=0.1350 | n_water=437 | time (s): 39.400 (total time: 271.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.930152 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.440395 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1358 0.0166 0.006 0.9 1.9 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.58 1.66 3.456 21.513 48.440 3.638 11.85 13.53 1.68 3.747 21.421 48.440 3.627 Individual atomic B min max mean iso aniso Overall: 9.28 104.62 21.25 2.20 209 1755 Protein: 9.28 104.62 17.07 2.20 0 1519 Water: 11.53 71.88 35.72 N/A 209 228 Other: 18.12 27.75 23.06 N/A 0 8 Chain A: 9.28 104.62 19.63 N/A 0 1755 Chain S: 15.37 59.61 34.83 N/A 209 0 Histogram: Values Number of atoms 9.28 - 18.81 1226 18.81 - 28.35 281 28.35 - 37.88 200 37.88 - 47.41 145 47.41 - 56.95 73 56.95 - 66.48 23 66.48 - 76.02 11 76.02 - 85.55 2 85.55 - 95.08 1 95.08 - 104.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1353 r_work=0.1185 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1354 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1350 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626179 | | target function (ml) not normalized (work): 302013.589828 | | target function (ml) not normalized (free): 15950.446368 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1182 0.1350 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1515 0.1515 0.1547 n_refl.: 87583 remove outliers: r(all,work,free)=0.1515 0.1515 0.1547 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1513 0.1513 0.1545 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1181 0.1348 n_refl.: 87583 remove outliers: r(all,work,free)=0.1188 0.1180 0.1348 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3945 299.773 267.341 0.476 1.000 0.308 11.894-9.307 97.06 95 4 0.2309 484.801 459.788 0.838 1.002 0.300 9.237-7.194 97.73 208 7 0.2456 384.357 380.128 0.917 1.002 0.170 7.162-5.571 100.00 427 22 0.2170 293.979 283.612 0.907 1.002 0.150 5.546-4.326 100.00 867 58 0.1138 403.560 399.068 0.952 1.002 0.140 4.315-3.360 100.00 1859 96 0.0934 383.789 381.523 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1142 252.129 250.337 1.001 1.002 0.120 2.608-2.026 99.99 8198 413 0.1022 167.139 166.205 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.622 81.885 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.194 35.828 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2122 22.805 21.444 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0344 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1180 r_free=0.1348 After: r_work=0.1180 r_free=0.1347 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.1183 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1350 | n_water=437 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1183 r_free=0.1350 | n_water=437 | time (s): 34.210 (total time: 36.100) Filter (q & B) r_work=0.1184 r_free=0.1352 | n_water=432 | time (s): 3.080 (total time: 39.180) Compute maps r_work=0.1184 r_free=0.1352 | n_water=432 | time (s): 1.420 (total time: 40.600) Filter (map) r_work=0.1206 r_free=0.1376 | n_water=320 | time (s): 2.520 (total time: 43.120) Find peaks r_work=0.1206 r_free=0.1376 | n_water=320 | time (s): 0.450 (total time: 43.570) Add new water r_work=0.1265 r_free=0.1446 | n_water=487 | time (s): 2.980 (total time: 46.550) Refine new water occ: r_work=0.1195 r_free=0.1361 adp: r_work=0.1195 r_free=0.1363 occ: r_work=0.1183 r_free=0.1348 adp: r_work=0.1182 r_free=0.1350 occ: r_work=0.1173 r_free=0.1338 adp: r_work=0.1170 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1170 r_free=0.1338 r_work=0.1170 r_free=0.1338 | n_water=487 | time (s): 139.480 (total time: 186.030) Filter (q & B) r_work=0.1178 r_free=0.1340 | n_water=446 | time (s): 3.560 (total time: 189.590) Filter (dist only) r_work=0.1185 r_free=0.1339 | n_water=444 | time (s): 37.140 (total time: 226.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.940060 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.461322 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1215 0.1379 0.0164 0.007 1.1 3.2 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 13.79 1.64 3.336 21.263 46.461 3.640 12.19 13.86 1.67 3.729 21.158 46.461 3.633 Individual atomic B min max mean iso aniso Overall: 9.27 100.54 21.03 2.04 217 1754 Protein: 9.27 100.54 16.78 2.05 0 1519 Water: 11.31 70.49 35.53 N/A 217 227 Other: 17.94 24.88 21.57 N/A 0 8 Chain A: 9.27 100.54 19.32 N/A 0 1754 Chain S: 15.53 58.59 34.81 N/A 217 0 Histogram: Values Number of atoms 9.27 - 18.40 1216 18.40 - 27.52 276 27.52 - 36.65 212 36.65 - 45.78 146 45.78 - 54.91 78 54.91 - 64.03 26 64.03 - 73.16 12 73.16 - 82.29 2 82.29 - 91.42 1 91.42 - 100.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1386 r_work=0.1219 r_free=0.1386 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1386 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1216 r_free = 0.1383 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1216 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.632672 | | target function (ml) not normalized (work): 302543.421511 | | target function (ml) not normalized (free): 15985.487601 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1473 0.1408 5.7405 5.6567| | 2: 3.57 - 2.84 1.00 2888 124 0.1132 0.1443 5.2063 5.2491| | 3: 2.83 - 2.48 1.00 2820 163 0.1242 0.1257 5.0155 5.0203| | 4: 2.47 - 2.25 1.00 2825 136 0.1041 0.1174 4.7168 4.7634| | 5: 2.25 - 2.09 1.00 2756 127 0.1004 0.1162 4.6572 4.741| | 6: 2.09 - 1.97 1.00 2846 113 0.0992 0.1207 4.3648 4.4813| | 7: 1.97 - 1.87 1.00 2787 165 0.1010 0.1343 4.0929 4.2462| | 8: 1.87 - 1.79 1.00 2789 144 0.1050 0.1253 4.0157 4.0893| | 9: 1.79 - 1.72 1.00 2745 138 0.0970 0.1303 3.737 3.8886| | 10: 1.72 - 1.66 1.00 2831 160 0.1016 0.1265 3.6527 3.7865| | 11: 1.66 - 1.61 1.00 2712 147 0.0976 0.1121 3.5889 3.6442| | 12: 1.61 - 1.56 1.00 2773 144 0.0933 0.1169 3.3663 3.4786| | 13: 1.56 - 1.52 1.00 2745 130 0.0998 0.1137 3.3552 3.4743| | 14: 1.52 - 1.48 1.00 2803 134 0.1007 0.1154 3.2767 3.3702| | 15: 1.48 - 1.45 1.00 2738 128 0.1017 0.1362 3.1816 3.335| | 16: 1.45 - 1.42 1.00 2756 161 0.1078 0.1306 3.1648 3.2669| | 17: 1.42 - 1.39 1.00 2785 139 0.1131 0.1312 3.126 3.2396| | 18: 1.39 - 1.36 1.00 2741 179 0.1150 0.1390 3.0906 3.2675| | 19: 1.36 - 1.34 1.00 2807 134 0.1227 0.1620 3.1031 3.2682| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1529 3.094 3.16| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1627 3.0923 3.1628| | 22: 1.29 - 1.27 1.00 2704 152 0.1466 0.1898 3.0879 3.2793| | 23: 1.27 - 1.26 1.00 2802 156 0.1572 0.1904 3.1056 3.2284| | 24: 1.26 - 1.24 1.00 2744 132 0.1613 0.1747 3.0944 3.1866| | 25: 1.24 - 1.22 1.00 2733 148 0.1783 0.2274 3.1098 3.2785| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1814 3.1211 3.2063| | 27: 1.21 - 1.19 1.00 2814 148 0.2009 0.2149 3.1385 3.1614| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2303 3.1387 3.1707| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2349 3.1284 3.2283| | 30: 1.16 - 1.15 1.00 2739 148 0.2378 0.2507 3.1171 3.1674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2922 171 0.95 9.08 1.00 0.97 6286.64| | 2: 3.57 - 2.84 2888 124 0.92 13.39 1.01 0.97 6286.64| | 3: 2.83 - 2.48 2820 163 0.89 17.57 0.99 0.97 5277.76| | 4: 2.47 - 2.25 2825 136 0.91 14.70 1.00 0.98 2676.18| | 5: 2.25 - 2.09 2756 127 0.89 16.90 1.01 0.98 2676.18| | 6: 2.09 - 1.97 2846 113 0.91 13.85 1.02 0.98 1586.40| | 7: 1.97 - 1.87 2787 165 0.94 11.13 1.02 0.98 656.96| | 8: 1.87 - 1.79 2789 144 0.91 14.71 1.00 0.98 656.96| | 9: 1.79 - 1.72 2745 138 0.93 11.74 0.99 0.98 354.67| | 10: 1.72 - 1.66 2831 160 0.93 12.56 0.98 0.98 294.13| | 11: 1.66 - 1.61 2712 147 0.92 13.25 0.99 0.98 280.80| | 12: 1.61 - 1.56 2773 144 0.95 9.90 0.99 0.97 155.08| | 13: 1.56 - 1.52 2745 130 0.94 11.50 1.02 0.97 155.08| | 14: 1.52 - 1.48 2803 134 0.94 11.64 1.02 0.98 138.25| | 15: 1.48 - 1.45 2738 128 0.95 10.70 1.01 0.98 107.43| | 16: 1.45 - 1.42 2756 161 0.94 11.97 1.02 0.98 107.43| | 17: 1.42 - 1.39 2785 139 0.94 11.65 1.01 0.98 96.41| | 18: 1.39 - 1.36 2741 179 0.94 11.99 1.01 0.99 90.03| | 19: 1.36 - 1.34 2807 134 0.94 12.54 1.00 0.99 90.03| | 20: 1.34 - 1.32 2696 147 0.94 12.57 0.99 0.97 84.15| | 21: 1.32 - 1.30 2785 112 0.93 13.52 0.99 0.97 83.73| | 22: 1.29 - 1.27 2704 152 0.93 14.00 0.99 0.97 83.82| | 23: 1.27 - 1.26 2802 156 0.92 14.92 0.98 0.95 84.24| | 24: 1.26 - 1.24 2744 132 0.92 15.10 0.97 0.95 84.24| | 25: 1.24 - 1.22 2733 148 0.91 16.47 0.97 0.95 85.70| | 26: 1.22 - 1.21 2727 135 0.90 18.21 1.03 0.94 87.31| | 27: 1.21 - 1.19 2814 148 0.89 18.87 1.02 0.94 87.31| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.93 90.59| | 29: 1.18 - 1.16 2800 134 0.88 20.67 1.00 0.93 91.82| | 30: 1.16 - 1.15 2739 148 0.86 22.07 0.99 0.93 91.82| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 83.73 max = 6286.64 mean = 988.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.24| |phase err.(test): min = 0.00 max = 87.29 mean = 14.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1216 0.1383 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1533 0.1532 0.1578 n_refl.: 87580 remove outliers: r(all,work,free)=0.1533 0.1532 0.1578 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1530 0.1529 0.1576 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1224 0.1216 0.1385 n_refl.: 87580 remove outliers: r(all,work,free)=0.1224 0.1215 0.1385 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4049 299.773 264.133 0.463 1.001 0.324 11.894-9.307 96.08 94 4 0.2472 484.987 463.239 0.849 1.002 0.256 9.237-7.194 97.73 208 7 0.2632 384.357 375.921 0.900 1.003 0.173 7.162-5.571 100.00 427 22 0.2339 293.979 281.878 0.894 1.003 0.151 5.546-4.326 100.00 867 58 0.1237 403.560 398.189 0.951 1.003 0.118 4.315-3.360 100.00 1859 96 0.1014 383.789 380.929 0.995 1.002 0.112 3.356-2.611 100.00 3867 181 0.1197 252.129 250.224 1.002 1.002 0.053 2.608-2.026 99.99 8198 413 0.1056 167.139 166.160 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0996 81.622 81.846 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.194 35.828 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2114 22.805 21.432 0.984 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0408 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2612 0.1911 0.081 5.386 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1744 0.081 5.386 9.0 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1744 0.081 5.386 9.0 119.5 20.1 258 0.000 1_nqh: 0.1645 0.1745 0.081 5.386 9.0 119.5 20.1 258 0.003 1_weight: 0.1645 0.1745 0.081 5.386 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1210 0.1458 0.008 0.977 9.0 119.5 20.1 258 0.126 1_adp: 0.1242 0.1537 0.008 0.977 8.5 118.6 21.1 258 0.126 1_regHadp: 0.1247 0.1542 0.008 0.977 8.5 118.6 21.1 258 0.126 1_occ: 0.1247 0.1544 0.008 0.977 8.5 118.6 21.1 258 0.126 2_bss: 0.1244 0.1538 0.008 0.977 8.7 118.7 21.3 258 0.126 2_settarget: 0.1244 0.1538 0.008 0.977 8.7 118.7 21.3 258 0.126 2_updatecdl: 0.1244 0.1538 0.008 0.987 8.7 118.7 21.3 258 0.126 2_nqh: 0.1246 0.1538 0.008 0.987 8.7 118.7 21.3 258 0.129 2_sol: 0.1236 0.1504 0.008 0.987 8.7 118.7 23.6 426 n/a 2_weight: 0.1236 0.1504 0.008 0.987 8.7 118.7 23.6 426 n/a 2_xyzrec: 0.1232 0.1532 0.007 0.878 8.7 118.7 23.6 426 n/a 2_adp: 0.1209 0.1510 0.007 0.878 8.8 113.9 23.2 426 n/a 2_regHadp: 0.1209 0.1509 0.007 0.878 8.8 113.9 23.2 426 n/a 2_occ: 0.1209 0.1507 0.007 0.878 8.8 113.9 23.2 426 n/a 3_bss: 0.1205 0.1502 0.007 0.878 8.8 113.9 23.2 426 n/a 3_settarget: 0.1205 0.1502 0.007 0.878 8.8 113.9 23.2 426 n/a 3_updatecdl: 0.1205 0.1502 0.007 0.879 8.8 113.9 23.2 426 n/a 3_nqh: 0.1205 0.1502 0.007 0.879 8.8 113.9 23.2 426 n/a 3_sol: 0.1233 0.1498 0.007 0.879 8.8 113.9 22.0 441 n/a 3_weight: 0.1233 0.1498 0.007 0.879 8.8 113.9 22.0 441 n/a 3_xyzrec: 0.1237 0.1460 0.005 0.915 8.8 113.9 22.0 441 n/a 3_adp: 0.1210 0.1409 0.005 0.915 9.2 108.9 21.6 441 n/a 3_regHadp: 0.1210 0.1410 0.005 0.915 9.2 108.9 21.6 441 n/a 3_occ: 0.1207 0.1409 0.005 0.915 9.2 108.9 21.6 441 n/a 4_bss: 0.1196 0.1385 0.005 0.915 9.2 108.9 21.6 441 n/a 4_settarget: 0.1196 0.1385 0.005 0.915 9.2 108.9 21.6 441 n/a 4_updatecdl: 0.1196 0.1385 0.005 0.916 9.2 108.9 21.6 441 n/a 4_nqh: 0.1196 0.1385 0.005 0.916 9.2 108.9 21.6 441 n/a 4_sol: 0.1189 0.1350 0.005 0.916 9.2 108.9 21.4 437 n/a 4_weight: 0.1189 0.1350 0.005 0.916 9.2 108.9 21.4 437 n/a 4_xyzrec: 0.1193 0.1358 0.006 0.947 9.2 108.9 21.4 437 n/a 4_adp: 0.1185 0.1353 0.006 0.947 9.3 104.6 21.2 437 n/a 4_regHadp: 0.1185 0.1354 0.006 0.947 9.3 104.6 21.2 437 n/a 4_occ: 0.1182 0.1350 0.006 0.947 9.3 104.6 21.2 437 n/a 5_bss: 0.1180 0.1348 0.006 0.947 9.3 104.6 21.2 437 n/a 5_settarget: 0.1180 0.1348 0.006 0.947 9.3 104.6 21.2 437 n/a 5_updatecdl: 0.1180 0.1348 0.006 0.946 9.3 104.6 21.2 437 n/a 5_setrh: 0.1180 0.1347 0.006 0.946 9.3 104.6 21.2 437 n/a 5_nqh: 0.1183 0.1350 0.006 0.946 9.3 104.6 21.2 437 n/a 5_sol: 0.1185 0.1339 0.006 0.946 9.3 104.6 21.2 444 n/a 5_weight: 0.1185 0.1339 0.006 0.946 9.3 104.6 21.2 444 n/a 5_xyzrec: 0.1215 0.1379 0.007 1.065 9.3 104.6 21.2 444 n/a 5_adp: 0.1219 0.1386 0.007 1.065 9.3 100.5 21.0 444 n/a 5_regHadp: 0.1219 0.1386 0.007 1.065 9.3 100.5 21.0 444 n/a 5_occ: 0.1216 0.1383 0.007 1.065 9.3 100.5 21.0 444 n/a end: 0.1215 0.1385 0.007 1.065 9.3 100.5 21.0 444 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4912670_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4912670_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0800 Refinement macro-cycles (run) : 3407.0900 Write final files (write_after_run_outputs) : 77.3200 Total : 3489.4900 Total CPU time: 58.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:05 PST -0800 (1735452605.14 s) Start R-work = 0.1644, R-free = 0.1744 Final R-work = 0.1215, R-free = 0.1385 =============================================================================== Job complete usr+sys time: 3638.45 seconds wall clock time: 65 minutes 28.96 seconds (3928.96 seconds total)